Migrants board Border Patrol vans on the US-Mexico border in El Paso, Texas, on May 11, 2023.
CNN  — 

US Border Patrol separated some migrant children from their parents while the families were in custody amid overcrowding in facilities, according to a Friday court filing.

The filing, which is part of a years-long court case, underscores the humanitarian and logistical challenges facing the Biden administration following an increase in migrant families crossing the US-Mexico border. The uptick has strained already-overwhelmed facilities that are not intended to hold people, particularly families, for prolonged periods, and, in limited instances, required authorities to temporarily put children and parents in separate holding areas.

Over the course of site visits this summer, Dr. Paul Wise, a pediatrician, found that authorities at a border facility in Donna, Texas, separated children from parents while in custody. Some of the children were as young as 8 years old.

“Separated children included girls separated from mothers and boys separated from their fathers. None of the interviewed children had visited with their parents since they were separated, including children who had been separated for 4 days,” Wise wrote, adding that children “were not aware of any protocols that would allow them to request a visit with their parents.”

Border Patrol officials cited overcrowding at the short-term facilities as the reason for the separations. Families, single adults, and unaccompanied children are generally held in different holding pods.

In a statement, a Customs and Border Protection spokesperson maintained the agency prioritizes keeping families together “at every step of the immigration process and have protocols to that end.”

“CBP appreciates Dr. Wise’s oversight; we will continue to review the report and associated recommendations and will respond as appropriate,” the statement said.

The independent monitoring by Wise is part of a court-approved settlement agreement stemming from a lawsuit against the federal government dating back to the 1980s that challenged inadequacies in the treatment of children in government custody.

The separations detailed in the report are different from those that occurred under the Trump administration’s “zero tolerance” policy, when families remained separated and, in some cases, parents were deported without their children. In the rare instances in which children are separated from a parent in custody now, they are reunited and released together, said a CBP official, who called separation a “last resort.”

CBP is expected to keep families together during processing, but amid space constraints, may need to temporarily hold children in another pod while clearing space, the CBP official said, to avoid circumstances in which children are mixed in a crowded area with single adults.

“In the interest of keeping everyone safe, sometimes we’re having to make these decisions that are tough,” the CBP official added.

Still, circumstances in which children are separated from their parents in government custody remain troubling for advocates.

“The government’s operational challenges cannot be solved on the backs of children,” Neha Desai, senior director of immigration at the National Center for Youth Law, told CNN.

Federal authorities have been encountering more than 7,000 migrants daily on the US-Mexico border, nearing numbers not seen since the spring when a Covid-era restriction was on the cusp of expiring, according to a Homeland Security official.

The latest number of daily encounters paints a grim outlook for the fall as President Joe Biden ramps up his reelection campaign and Republicans continue to hammer the administration over its handling of border crossings.

In May, ahead of the expiration of the Covid-era restriction known as Title 42, US Customs and Border Protection encountered more than 8,000 people daily and had around 25,000 migrants in custody. But after Title 42 expired, numbers dropped dramatically as the administration levied consequences against those who crossed the border illegally.

“If we don’t find a way to decompress, that’s not going to change. It’s an unsafe situation for the migrants. It’s an unsafe situation for the people working in soft sided facilities,” the Homeland Security official said.

Since Biden took office, officials have set up additional soft-sided facilities similar to tent complexes to process the growing number of migrants crossing the border, but those facilities are not equipped to care for people long term. Many of those now crossing are also families – a vulnerable population that poses a unique challenge for officials.

Border arrests ebb and flow regardless of who is in the Oval Office. But deteriorating conditions in Latin America that were exacerbated by the coronavirus pandemic have contributed to people wanting to migrate to the United States.

The number of migrants crossing the treacherous Darién Gap – which connects Panama and Colombia and has recently served as a barometer for movement in the region – broke a record this year. According to authorities, 248,901 people crossed the jungle in 2023, and of those, approximately 20% are children and adolescents.

“We’re monitoring it really closely and are concerned,” a senior administration official previously told CNN. “This has been a high priority for the US and for our partners in the region.”

Michelle Watson and Josh Campbell contributed reporting.